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vps39 VPS39 subunit of HOPS complex [ Danio rerio (zebrafish) ]

Gene ID: 567078, updated on 4-Jan-2025

Summary

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Official Symbol
vps39provided by ZNC
Official Full Name
VPS39 subunit of HOPS complexprovided by ZNC
Primary source
ZFIN:ZDB-GENE-080530-2
See related
Ensembl:ENSDARG00000074471 AllianceGenome:ZFIN:ZDB-GENE-080530-2
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
lbk; vam6
Summary
Acts upstream of or within developmental pigmentation; eye development; and vesicle-mediated transport. Is expressed in brain; digestive system; head; and integument. Orthologous to human VPS39 (VPS39 subunit of HOPS complex). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
human mouse all
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Genomic context

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See vps39 in Genome Data Viewer
Location:
chromosome: 17
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (50073970..50113486)
105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (49994882..50034417)

Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene zgc:100951 Neighboring gene zgc:173816 Neighboring gene UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16 Neighboring gene Jun dimerization protein 2a

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles. Schonthaler HB, et al. Development, 2008 Jan. PMID 18077594
  2. Nxhl Controls Angiogenesis by Targeting VE-PTP Through Interaction With Nucleolin. Luo H, et al. Front Cell Dev Biol, 2021. PMID 34733844, Free PMC Article
  3. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
  4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The present study provides the first phenotypic description of a lack of vam6 gene function in a multicellular organism.
    Title: The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
acts_upstream_of_or_within developmental pigmentation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within eye development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
vam6/Vps39-like protein
Names
vacuolar protein sorting 39 homolog
vesicle fusion protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001113540.2 → NP_001107012.2  vam6/Vps39-like protein

    Status: VALIDATED

    Source sequence(s)
    CU655820, CU928140, EF446162
    UniProtKB/TrEMBL
    A0A8N1YZ39, B0EXK3
    Related
    ENSDARP00000100792.2, ENSDART00000113644.4
    Conserved Domains (4) summary
    pfam00637
    Location:579 → 734
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:448 → 550
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:760 → 868
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20 → 278
    CNH; CNH domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007128.7 Reference GRCz11 Primary Assembly

    Range
    50073970..50113486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005158918.5 → XP_005158975.1  vam6/Vps39-like protein isoform X1

    UniProtKB/TrEMBL
    A0A8M2B5G7, B0EXK3
    Conserved Domains (4) summary
    pfam00637
    Location:578 → 733
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:447 → 549
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:759 → 867
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20 → 277
    CNH; CNH domain
Nucleotide Protein Strain
Heading Accession and Version

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